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Emi Sei

As seen in: Nature, Genome Biology, Cell Press, Cell Reports, Texas Medical Center
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Articles by Emi Sei

Ecotypes of triple-negative breast cancer in response to chemotherapy

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By Yun Yan, Yiyun Lin, Tapsi Kumar, Shanshan Bai, Aatish Thennavan, Jianzhuo Li, Emi Sei, TUẤN TRẦN, Tuan Tran, Min Hu, Mitchell Rao, Chenling Tang, Siyuan He, Anna K Casasent, Debu Tripathy, Alastair Thompson, Lei Huo, Stacy L. Moulder, Clinton Yam, Nicholas E Navin, Elizabeth Ravenberg, Gaiane Margishvili Rauch, Alyson R. Clayborn
| Nature Verified
Abstract Triple-negative breast cancer (TNBC) is an aggressive subtype that is frequently treated with chemotherapy, but only half of the patients respond well and have good clinical outcome1,2. Here we leveraged pretreatment tissue samples from treatment-naive patients with TNBC who received neoadjuvant chemotherapy and performed single-cell transcriptomic analysis of 427,857 cells from 101 patients and spatial transcriptomic analysis of 44 patients.
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Delineating the copy-number substructure of metastatic tumors with CopyKit

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By Junke Wang, Darlan Conterno Minussi, Alexander Davis, Runmin Wei, Hanghui Ye, Emi Sei, Aislyn Schalck, Yun Yan, Hua-Jun Wu, Shanshan Bai, Cheng Peng, Min Hu, Anna K Casasent, Alejandro Contreras Verified, Hui Chen, David Y. Hui, Senthil Damodaran, Mary Edgerton, Scott Kopetz, Nicholas E Navin
| Cell Press Verified
Keywords single-cell genomics scDNA-seq copy-number analysis computational ploidy estimation tumor evolution intratumor heterogeneity metastasis cancer genomics Introduction Advances in single-cell DNA sequencing (scDNA-seq) technologies for copy-number profiling have led to vast decreases in costs and experimental worktime, while greatly improving the data quality and cell throughput.
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The impact of breast radiotherapy on the tumor genome and immune ecosystem

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By Aislyn Schalck, TUẤN TRẦN, Tuan Tran, Jianzhuo Li, Emi Sei, Shanshan Bai, Min Hu, Jerome Lin, Scott Bright, Samuel Reddick, Harsh Batra, Alejandro Contreras Verified, Maria Gabriela Raso, Michael C. Stauder, Karen E. Hoffman, Jay Reddy, Kevin T Nead, Benjamin Smith, Gabriel O. Sawakuchi, Wendy A. Woodward, Stephanie S. Watowich, Jennifer K. Litton, Isabelle Bedrosian, Elizabeth A. Mittendorf, Huong T. Le-Petross, Nicholas E Navin, Simona F. Shaitelman
| Cell Reports Verified
Keywords single cell genomics breast cancer radiation tumor microenvironment Research topic(s) CP: Cancer Introduction Radiotherapy is a component of oncologic treatment for the majority of breast cancer patients.
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Spatial Charting of Single-Cell Transcriptomes in Tissues

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By Runmin Wei, Siyuan He, Shanshan Bai, Emi Sei
| Texas Medical Center
To view the content in your browser, please download Adobe Reader or, alternately, you may Download the file to your hard drive. NOTE: The latest versions of Adobe Reader do not support viewing PDF files within Firefox on Mac OS and if you are using a modern (Intel) Mac, there is no official plugin for viewing PDF files within the browser window.
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"Single-Cell Sequencing Reveals Trajectory of Tumor-Infiltrating Lympho" by Aislyn Schalck, Donastas Sakellariou-Thompson et al.

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By Aislyn Schalck, Marie-Andrée Forget, Emi Sei, Donastas Sakellariou-Thompson
| Texas Medical Center
Pancreatic ductal adenocarcinoma (PDAC) has few effective treatments. Immunotherapy, an attractive alternative strategy, remains challenging with the lack of knowledge on the tumor-infiltrating lymphocyte (TIL) landscape in PDAC. To generate a reference of T-cell subpopulations, we profiled 80,000 T cells from 57 PDAC samples, 22 uninvolved/normal samples, and cultured TIL using single-cell transcriptomic and T-cell receptor analysis.
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Decoding the evolutionary response to prostate cancer therapy by plasma genome sequencing

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By Nicholas E Navin, Naveen Ramesh, Emi Sei, Pei Ching Tsai
| Genome Biology Verified
Naveen Ramesh1,2, Emi Sei1, Pei Ching Tsai3, Shanshan Bai3, Yuehui Zhao1, Patricia Troncoso4, Paul G. Corn3,5, Christopher Logothetis3,5, Amado J. Zurita3,5 na1 & Nicholas E. Navin ORCID: orcid.org/0000-0002-2106-86241,2,5,6 na1 Genome Biology volume 21, Article number: 162 (2020) Cite this article Abstract Background Investigating genome evolution in response to therapy is difficult in human tissue samples.
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Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing

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By Charissa Kim, Ruli Gao, Emi Sei, Rachel Brandt
| Cell Press Verified
Triple-negative breast cancer (TNBC) is an aggressive subtype that frequently develops resistance to chemotherapy. An unresolved question is whether resistance is caused by the selection of rare pre-existing clones or alternatively through the acquisition of new genomic aberrations. To investigate this question, we applied single-cell DNA and RNA sequencing in addition to bulk exome sequencing to profile longitudinal samples from 20 TNBC patients during neoadjuvant chemotherapy (NAC).
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Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing

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By Anna K Casasent, Aislyn Schalck, Ruli Gao, Emi Sei
| Cell Press Verified
Ductal carcinoma in situ (DCIS) is an early-stage breast cancer that infrequently progresses to invasive ductal carcinoma (IDC). Genomic evolution has been difficult to delineate during invasion due to intratumor heterogeneity and the low number of tumor cells in the ducts. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS) to measure genomic copy number profiles of single tumor cells while preserving their spatial context in tissue sections.
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